A former Stanislaus Superior Court clerk accused of stealing thousands in cash from court fee payments pleaded not guilty during his arraignment hearing Wednesday afternoon.

Barry James Lesko of Modesto has been charged with felony counts of embezzlement by a public official and altering or destroying court records while on the job. Lesko is accused of stealing at least $2,400.

Superior Court Judge John Whiteside scheduled Lesko to return to court April 1 for a pretrial hearing. Lesko, a nine-year employee, worked at the court’s traffic division office on Floyd Avenue in east Modesto.

Another former court clerk, Dawn Marie Rios of Riverbank, also has been charged with felony counts of embezzlement by a public official and altering or destroying court records while on the job. She is scheduled to return to court April 1 for a continued arraignment hearing.

Police investigators have said the defendants accepted court fee payments and marked them as paid, but later voided the transactions so they would not show on the register.

The investigation into Lesko began when a woman discovered she was sent to collections for failing to pay a court fee. She provided proof of payment to the court.

The defendants were arrested in late September. The Stanislaus County District Attorney’s Office filed criminal complaints against them Feb. 5.

The investigators also have said it appears Rios and Lesko were not working together on the embezzlement schemes, though detectives say the money was stolen in a similar fashion. The defendants are being prosecuted separately.

Rios is accused of stealing at least $4,000 last year. She worked as a clerk at the downtown Modesto courthouse for 10 years and was responsible for collecting court filing fees.

Rios and Lesko have resigned from their jobs, according to court officials. They remain out of jail while awaiting prosecution.